Severed
by LMXB
Summary: This is set several weeks in the future. After the other Supergirl has shown up and started destroying Kara's reputation, Kara finds herself battling with Alex who has lost all faith in Supergirl.
1. Chapter 1

**Disclaimer**: I don't own Supergirl or the characters. This is written purely for fun.

**A/N:** This is set in Season 4 several weeks further ahead than the show is now. As such there are a few assumptions:

1\. The other version of Supergirl has emerged and by pretending to be Supergirl when committing evil acts the city and Alex believe that Supergirl has turned.

2\. The mind wipe has continued to have unexpected consequences and Alex and Kara are drifting apart.

3\. Lena has found out that Kara is SG and has not taken it well. Their friendship is in tatters and Lena has become isolated.

Despite all of the above and the events of the first few chapters this will have a happy (ish) ending.

* * *

"Hey guys, what are you doing her?" Alex asked when she found J'onn and Kara waiting on her doorstep.

"Alex, we need to talk to you." J'onn said.

"Sure, what's up?" Alex asked letting them in.

"It's about Supergirl."

"What about her?" Alex asked wearily.

"She's not the enemy." J'onn stated.

"Isn't she? Because when people start killing my Agents I see them as the enemy."

"That wasn't Supergirl." Kara said.

"It sure looked like Supergirl, sounded like Supergirl and had Supergirl's powers. So my money is on Supergirl." Alex argued.

"Supergirl wouldn't do that." Kara argued.

"Only she did. And it's not the first time she's gone off the rails. I have a break in my arm thanks to her." Alex remind her almost causing Kara to flinch at the harshness of her words.

"What happened back then was a result of Maxwell Lord, it wasn't Supergirl's fault." J'onn said.

"Maybe, but it was a warning of how dangerous she could be. A warning we all ignored. And because we ignored it people are dying." Alex said.

"It's not her. There's another explanation." Kara said.

"Like what? A twin sister? Her version of Reign?" Alex asked. "No if there was ever an example of Ockham's razor being needed it's here. The simplest explanation is Supergirl has turned."

"Think about it Alex, why would she?" J'onn asked.

"Perhaps her ego took a hit when the President showed she wasn't vital to the DEO?" Alex suggested. "Or perhaps she is high on some crazy Kryptonite. Or maybe she got disillusioned by the Children of Liberty. All I know is she is a threat and we need to stop her."

"Supergirl is not responsible and she is not the enemy." Kara said.

"Kara, you don't understand." Alex said. "This is what I do. And I'm good at my job. So how about rather than trying to push your beliefs onto me, you trust my judgement."

"You really believe that Supergirl is responsible?" Kara asked looking Alex in the eyes. "That she's a killer?"

"Yes." Alex said with no trace of doubt in her voice. The answer feeling like a punch to Kara.

"Well there is no point in talking about this further." Kara said trying to hide how upset she was. "I better go. And Alex, I have an assignment out of the city so I won't be around for awhile." With that she hurried from Alex's apartment.

"Kara, wait." Alex called but when the door shut she looked at J'onn and asked.

"What's up with her?"

"She knows Supergirl is innocent and she wants you to believe it."

"Then bring me proof." Alex said. "You know I trust your judgement, but I also trust mine. And right now I have no reason to believe Supergirl hasn't turned."

"Alex, just promise me you won't do anything you'll regret. Killing is never the answer." J'onn said.

"You didn't use to feel like that." Alex said. "I will do what it takes to keep this country safe. And right now that includes stopping Supergirl, by any means necessary."

-00-

"You okay?" J'onn asked when he met Kara by his car.

"Yeah." She said, but as J'onn kept looking at her she shook her head and said. "No."

"Come here." He said pulling her into his arms.

"Was any of it real?" Kara asked.

"Of course it was. Alex loves you."

"Well she hates half of me." Kara said pulling away.

"She doesn't hate Supergirl." J'onn said. "But she has lost faith in her, which is why I think you should leave."

"I just told Alex I was going away for awhile."

"As Kara. I mean both parts of you should stay away." J'onn clarified.

"I'm not running away."

"The DEO are developing weapons that can kill you with a single shot."

"I know that. But although Alex has lost faith in me, I still have faith in Alex. And I'm not leaving her unprotected when there is an evil me running around out there. Besides anyone who wants to can get a gun that could kill Alex with a single shot. She has always had my back and right now whether or not she is willing to accept it she needs me to have hers."

"Okay, just promise me you'll be careful." J'onn asked.

"I promise." Kara said.

"Something else on your mind?" J'onn asked.

"I get her not liking Supergirl. I mean it hurts, but I kind of get it. But I had hoped by now we would have started connecting again."

"The other you isn't helping with that." J'onn said.

"I don't mean Supergirl and Alex, I mean Alex and I. Every day we drift further apart." Kara said sadly.

"You are keeping your distance as much as she is." J'onn reminded her.

"I'm keeping my distance to stop her figuring out who I am and to her allow herself to get everything she wants. She's keeping her distance because she wants to. Do you know when we last had a sisters' night?"

"No."

"Neither to I. I miss my sister." Kara said sadly as her phone buzzed. "I have to go." She said having read the message.

-00-

"Where have you been?" Nia asked when she opened her door to Brainy.

"At work." He replied. "My absence would be noticed, even when I multitask."

"I know. I'm sorry. But I need your help and I don't know if I should tell Kara. I mean I know I should, but it'll break her." She said pacing.

"Break her?"

"Well how would you feel if your sister killed you?"

"Alex is going to kill Kara?" Brainy asked eyes wide.

"Yes. No. I mean I don't know. I had a dream that Alex killed Supergirl."

"This is bad." Brainy agreed. "How did she kill her?"

"She shot her. It was a gun I didn't recognise, but that could have been symbolic. I still suck at this interpretation thing." Nia said. "Should I tell Kara? I mean she is going to get so upset and she is already upset."

"No." Brainy said. "Don't tell Kara. I will work on something. For now just tell me everything you saw. No detail is too insignificant."

**-TBC...**

* * *

**A/N:** Thanks for reading and reviewing.


	2. Chapter 2

A/N: Thanks for the comments.

Guest (1) - Supergirl has no intention of dying in this chapter.

Guest (2) - The 'how' of Lena finding out isn't really important in the story and as everyone seems to have their own preferred method I will leave it to the reader to decide. 'Evil' Supergirl is only appearing as Supergirl, not Kara, she is more concerned with ruining Supergirl's reputation than Kara's. But the focus of the story is not how they got to the current state but how they fix things.

Guest (3) - The other Supergirl has been around for awhile so you can assume all those arguments have been had before this story starts. I genuinely have no idea with this crazy mind wipe plot how much Alex will know about the multiverse seeing it is so tied to Kara being Supergirl.

* * *

"Hi Nia." Kara said approaching her on a CatCo balcony.

"Kara. Hi." Nia responded more jumpy than normal.

"Is everything okay?" Kara asked.

"It's fine." Nia said.

"You sure, it feels like you have been avoiding me."

"Yes...I mean no. I'm just trying to study interpretation and it is really hard and taking up all my time." Nia half lied.

"Have you tried talking to your sister?" Kara asked.

"No. She is still angry at me and I can't ask for help. I mean it would be like slapping her in the face." Nia said sadly as Kara's phone rang.

"Kara." Brainy said on the phone before Kara had a chance to say anything.

"Hey Brainy, what's up?"

"There is a fight breaking out at a gas station between the Children of Liberty and some hostile aliens. The other you is also there."

"I'm on it." Kara said looking round before changing into Supergirl and jumping off the balcony.

"You must exercise caution, Alex is on route with the new DEO weapon. A weapon designed to kill you."

"I know. But I also know that Alex wouldn't use it." Kara said as she flew to the location Brainy sent her.

"I hope you are right." Brainy said.

"I am. Deep down Alex is still Alex." Kara said with no doubt in her voice. As she approached the gas station a huge explosion went off causing Kara to momentarily stop.

"This is bad." Kara said said before flying at full speed towards the fire.

-00-

"Give me a sitrep." Alex said as she drove towards the latest sighting of Supergirl going crazy.

"The gas station has just exploded." Brainy said. "The public have already evacuated the nearby area. The fear of being attacked out weighs their dodo like instinct to tweet everything." Brainy said. "However, the Children of Liberty and the aliens may still be there. And are likely to be hostile."

"What caused the explosion?" Alex asked.

"There is insufficient data."

"Brainy." Alex growled.

"It would appear heat vision was used to ignite the petroleum." Brainy told her.

"So Supergirl is responsible?" Alex asked.

"Or a doppelgänger." Brainy said. "The video evidence merely shows a flying alien with blond hair and a red cape...and glowing eyes."

"One crazy Kryptonian is enough for me." Alex said. "I'll be there shortly."

"Director Danvers, please be careful." Brainy warned.

"Don't worry, I have your new weapon and the squad will be here soon." Alex said as she approached the blaze at the gas station.

"That is not what I meant." Brainy said.

"Just when I thought she couldn't get any worse." Alex said bringing her bike to a stop close to Supergirl who was standing over a charred body.

"So now you hang around and gloat at your victims?" Alex asked as she jumped off her bike and removed her helmet.

"I didn't do this." Supergirl said.

"Do you think I'm stupid?" Alex asked. "You were caught on tape." She added pointing to a CCTV camera.

"That wasn't me. You know me Alex, I wouldn't do this."

"I don't know you." Alex said. "But I am taking you in. Then the Truth Seeker can figure out what you have done. If you're innocent it will prove it."

"And reveal who I am? Endangering everyone I love." Supergirl said.

"So you don't trust us but want us to trust you?" Alex asked pulling a gun on Supergirl."

"What are you doing?" Kara Supergirl asked.

"Taking you in. This weapon will kill you so just surrender." Alex said as Supergirl saw an armed alien appear behind Alex.

"Watch out." She cried as she used her heat vision on the alien. Misinterpreting Supergirl's target Alex instinctively fired the weapon, hitting Supergirl. Realising the heat vision hadn't hit her Alex turned and saw a fallen alien clutching his shoulder behind her before turning back to Supergirl who dropped to her knees.

Before Alex could say anything another figure landed next to Supergirl and pushed Kara's head so she fell and lay sprawled on the ground.

"You shot her." The double of Supergirl said looking at Alex. But as Supergirl stopped moving the alternate version used her super hearing to confirm no heart beat and added. "Scratch that. You killed her. You really don't like the Zor-El family do you? First Aunt Astra and now her. If only I had been here a few seconds earlier I would have heard her heart rip in two when she realised you have no feelings for her."

"Who are you?" Alex asked confused.

"Her evil twin."

"You've been responsible for everything?" Alex asked.

"Apart from Supergirl's murder, that's on you. I just wanted to destroy her reputation and send her into hiding so I could take over this country unopposed. But your method is so much cleaner. So instead of killing you. I'll just thank you." With that she took to the skies moments before J'onn landed at speed next to Kara's lifeless body.

"What happened?" J'onn asked.

"I shot her." Alex said.

As J'onn picked the lifeless Supergirl up he looked at Alex with disappointment in his eyes.

"I didn't know." Alex said.

"I told you she wasn't responsible and I told you not to use lethal force." He said.

"Where are you taking her?"

"Somewhere where she can have he funeral she deserves and not be treated like a DEO experiment." He said before flying off.

**-TBC...**

* * *

**A/N:** Thanks for reading and reviewing.


	3. Chapter 3

A/N: Thanks for the comments.

Flash4818 - Alex will feel lots of angst and remorse and guilt as this goes on. The next few chapters will be sad, but I promise it will get happier.

Guest (1) - I will not be using the ring of ludicrous magic in this (or probably any other) story. I am assuming in this (and in the show) that Eliza will have been told, else there would be many awkward conversations.

Chloe - Everything that has happened in the show up until the last episode is assumed to have happened, so yes Supergirl did burn Alex's hand.

Kira007 Goddess of Chaos - It will be awhile before Alex discovers the truth and then she will suffer.

Guest(2) - I know it doesn't do much good now, but I aim to get updates posted daily.

Alexkarafan - There will be lots of guilt from Alex in later chapters.

Guest(3) - It probably won't be the last.

* * *

"Oh Kara." Eliza said as she and J'onn entered the Fortress of Solitude where Kara was lying unmoving on a slab, with Brainy by her side.

"You are just in time." Brainy said. "She should wake at any moment."

"Will she be okay?" Eliza asked, still holding onto J'onn, desperate for support.

"Physically she will be fine. Probably." Brainy said.

"Emotionally it is a different story." J'onn said. "Ever since I wiped Alex's mind, Kara has become more withdrawn and now this." Before Eliza could respond Kara sat up gasping for breath.

"Kara." Eliza said rushing to her side. "It's okay. You're okay." She said hugging her.

"Eliza?" Kara asked confused, feeling disorientated. "Where am I? What happened?"

"You are at the Fortress of Solitude." Brainy said.

"Alex shot me." Kara said looking down at her chest. "How am I alive? You said the DEO weapon would kill me?"

"Nia had a dream that Alex would shoot you. So when I was ordered to make the weapon I may have redefined my orders and ensured it would not be fatal to you. Merely stop your heart for thirty minutes so you could be brought her and revived." Brainy said.

"But Alex thought it would kill me?" Kara asked.

"Yes." Brainy said. The answer causing Kara to look more defeated than J'onn had ever seen her.

Not knowing what to do Eliza just pulled her in for a hug.

"There is some good news though." Brainy said.

"What?" Kara asked pulling away from Eliza.

"After you were killed, the other version of you showed up. So now the world believes that you are not the evil Supergirl."

"They still believed it. Alex believed it." Kara said sadly.

"Can you leave us?" Eliza asked looking at Brainy and J'onn.

"Of course." J'onn said leading Brainy outside of the Fortress. Once they were alone Eliza once again pulled Kara into her arms, holding her daughter as Kara broke down in tears.

"She hates me. I feel so alone." Kara said when she finally stopped crying.

"Alex's issues are with Supergirl not Kara." Eliza tried.

"We're not close anymore. It's like when I first came to Earth. It feels like Alex tolerates my presence but sees me as a burden. I tried spending more time with her at first, hoping to make new memories, but that just made it worse. So I gave her space. And now she doesn't even call anymore. I know I can talk to you and Nia and Brainy and J'onn but..." She trailed off.

"But it's not the same." Eliza finished for her.

"I miss her so much." Kara said sadly as Eliza held her again.

"I know you do." Eliza said unsure of how she could help Kara. "I know it doesn't feel like it right now, but you are not alone. You are surrounded by people who love you. Don't forget that."

-00-

As Alex sat in her apartment drinking whiskey, once again trying to figure out why it felt like she was missing something there was a knock at her door. Frowning she picked up her side arm and looked through the peep hole. On seeing who it was she stood silently unsure what to do. But then the visitor knocked again and shouted.

"I know you are in there. I'm not leaving."

Sighing Alex opened the door and asked.

"Maggie? What are you doing here?"

"I thought you may need someone to talk to and I know there aren't that many people you can tell."

"Talk to? About what?" Alex asked confused as she stepped away from the door.

"You killing Supergirl." Maggie said.

"I've been cleared of any wrong doing." Alex said slightly defensively.

"Okaaaaay. But I know how hard it will be to lose Kara."

"Kara? What does Kara have to do with this?" Alex asked.

"What do you mean what does Kara have to do with this?" Maggie asked growing concerned for Alex's sanity.

"Kara wasn't even in the city." Alex said as her phone buzzed. "I have to go, the other Supergirl has shown up again."

-00-

"Maggie? What are you doing here?" James asked.

"I need to talk to you." She said entering the office and shutting the door.

"Sure, what's up?"

"I saw Alex yesterday and I'm really worried about her."

"She's struggling with killing Supergirl?" James guessed.

"No the complete opposite, she treated it like business as normal and then acted like she didn't know that Supergirl was Kara."

"She doesn't." James said.

"What?" Maggie asked eyes wide.

"It's complicated, but there is a Colonel providing oversight at the DEO and she is obsessed with finding out Supergirl's identity. She brought in some mind reading alien which couldn't be defeated, so everyone at the DEO who knew her identity, including Alex, agreed to have their minds wiped by J'onn." James explained.

"So Alex has no idea she just killed Kara?"

"No."

"It's going to kill her if she ever finds out." Maggie pointed out.

"I don't know what the plan is, but it might be they never tell her."

"That's not the right choice." Maggie argued.

"It's not our choice to make." James countered.

"Won't she figure it out when she realises that Kara is dead?"

"Honestly, I don't know. It's complicated." James said. "J'onn had to erase all memories of Kara being an alien, which meant that Alex kind of lost her connection to Kara. I mean Alex is still protective but somehow they have just drifted. Kara started to spend less time round Alex so she didn't figure out who she was and then she hoped if they spent less time round each other Alex would go after what she really wanted in life."

"And Alex just let Kara drift away?" Maggie asked.

"Yes."

"This is really messed up." Maggie said.

-00-

"What now?" J'onn asked as he came and sat next to Kara who was staring at a crystal.

"I don't know."

"The world thinks Supergirl is dead. You don't have to go back." J'onn said. "I could take you to Argo City, you could live with your mother."

"No I can't. There is an evil version of me flying round and Alex is out there. I need to look after her."

"She may not want your help." J'onn said as gently as possible.

"I know. But I don't care. I'm not going to leave her defenceless."

"Kara, if you return we don't know how Alex will react." J'onn tried again. "I know you are going to protect Alex, but to that, openly returning as Supergirl may not be the best option."

"Then I won't return as Supergirl. I can go back as Kara and look out for her."

"The other version of you will know who you are. To protect Alex I think you have to stay hidden until we know how to defeat the other you."

"And to do that you are going to need help." Brainy said joining them. "Fortunately I have an idea."

**-TBC...**

* * *

**A/N:** Thanks for reading and reviewing.


	4. Chapter 4

A/N: Thanks for the comments.

Chloe - Maggie will make another appearance but the focus will be on the sisters rather than anyone else. James doesn't know she is alive. More clarification on who knows what in this chapter.

Guest (1) - Alex will have a bad reaction. Eventually.

Guest (2) - I'd assume Kara would use a phone and warn Eliza. The only reasons I could see for the writers not to do that are either, they forget or they want a comedy episode later on where Eliza comes to town and Kara realises she hasn't told her.

DanversSisters - Some other events will happen before she gets her memories back, which will influence how she reacts.

* * *

"Brainy, what are you doing here?" Lena asked when he entered her office at L-Corp.

"Seeking your help." He said.

"With what?" Lena asked curious.

"The other Supergirl." He said. "We need a way to stop her."

"Isn't that what the DEO is working on?" Lena asked.

"Yes, but their approaches will be fatal. We need a solution that doesn't kill her."

"Why?"

"Supergirl doesn't kill." Brainy said.

"Supergirl is dead." Lena pointed out as Kara walked into her office. "Or not. You really are full of secrets."

"Only four people know that I'm alive. Eliza, J'onn, Brainy and you."

"What about Alex?"

"We have no reason to tell her." Brainy said.

"No reason to tell her? Doesn't she think she just killed her sister?" Lena asked.

"She doesn't know I'm Supergirl." Kara said.

"How is that possible?" Lena asked.

"J'onn wiped her memories." Kara explained.

"When? Why?"

"A few weeks ago she had them wiped to protect me and the people I care about." Kara said.

"A few weeks?" Lena asked surprised.

"Yes."

"Around the time she forgot what your favourite movie was?" She guessed.

"Yes." Kara confirmed before trying to move the conversation along. "I need a way to defeat the other me. I can't do it alone. I can't go to the DEO. You are my only hope. I know you don't want to help me, but I also know you don't want to see innocent people get hurt. So for their sake please help us stop the other me."

-00-

"Where have you been?" Alex asked as she approached Brainy.

"Seeking information regarding the other Supergirl." He said.

"Did you find anything?" Alex asked.

"No. Not so far."

"Keep searching." Alex said.

"Of course." Brainy confirmed before asking. "How are you doing?"

"I'm fine. Why?"

"You seem a little distracted."

"Well I feel like I am missing something. Until I have figured out what it will be hard to concentrate."

"Have you spoken to J'onn?"

"I tried. But he just had a disappointed look in his eyes. I can't deal with that now." Alex said. "I'm going to brief Haley. Let me know if you find anything."

"Of course."

-00-

"Why are you hiding?" Brainy asked when he entered Nia's apartment.

"Because I don't know what to do any more. What is the point of this power. I couldn't use it to save my mother and I couldn't use it to save Kara."

"But you did." Brainy said.

"No I didn't. Kara was killed, by her own sister. What happens of Alex ever figures that out? It will break her and that will be three lives I failed to save."

"Nia, your information did save Kara."

"What?"

"As a result of what you told me I modified the DEO weapon. It merely stopped Kara's heart for thirty minutes. Fortuitously the other Supergirl was there to so everyone now believes that Supergirl is not the enemy, just that she's dead. Which is good as it buys us time."

"Kara's alive?" Nia asked.

"Indeed. She is at L-Corp helping Lena develop a weapon capable of stopping the other version of herself."

"Kara's alive and you are only telling me this now?" Nia asked jumping up.

"Where are you going?" Brainy asked confused.

"To see Kara."

-00-

"I need to take some blood." Lena said as she approached Kara in the lab at L-Corp.

"Which means Kryptonite?" Kara guessed.

"Yes." Lena replied causing Kara to hold out her arm.

"Just like that?" Lena asked as she inserted the Kryptonite needle in Kara's arm. "You didn't trust me with your identity, but you trust me enough to stab you with a Kryptonite needle?"

"Not telling you wasn't to do with trust, it was me trying to keep you safe. I never meant to hurt you and I will always regret that I did. But I know you are a good person and I will always trust you." Kara said as Lena withdrew the needle. As she put the vials of blood on a tray the door opened.

"Kara, you're okay!" Nia said as she entered the room with Brainy.

"Nia?" Kara asked confused.

"I told her you were alive, but apparently she didn't believe me." Brainy explained.

"I'm sorry I didn't tell you sooner." Kara apologised meekly.

"You had enough to worry about. And you've put my problems into context, I mean at least my sister didn't actually try to kill me." Nia said. "Sorry, that was tactless."

"It's okay." Kara said. "I mean it's not, but it's true."

"I'll leave you to catch up." Lena said leaving the room.

"How's Alex?" Kara asked Brainy.

"She is … okay." He said non-committally.

"Look after her for me?" Kara asked.

"Of course. J'onn is also watching over her." He assured her.

"Don't suppose you've had any dreams of me defeating the other me?" Kara asked Nia hopefully.

"No. Not yet. I'm sorry." Nia said. "But I promise you next time I will tell you straight away."

"Brainy told me why you didn't." Kara said. "I understand. I wouldn't have believed you anyway."

-00-

"How is your research going?" Brainy asked as he approached Lena.

"Slowly." Lena said.

"Would you like some assistance?" He offered.

"Sure. You can just magic up a solution using your knowledge of the future." Lena replied.

"I wish it were that simple." Brainy said. "Even if I did have a solution I could not share it."

"Tell me, are things progressing as you are expecting?"

"I do not know the events in detail." Brainy replied. "So I can not answer that. But this world is darker than I was expecting." He then paused and said. "I would like to thank you."

"For what?"

"Your box solution is most effective."

"You're welcome." Lena said.

"I should you warn you though, Nia does not think it leads to long term happiness."

"Some of us don't have the luxury of assuming we deserve long term happiness." Lena said. "Now if you'll excuse me I have a meeting to get to."

**-TBC...**

* * *

**A/N:** Thanks for reading and reviewing.


	5. Chapter 5

A/N: Thanks for the comments.

Chloe - I'm still not entirely sure Kara didn't kill the Fort Rozz guard. It sounded like his neck snapped. J'onn is also being a bit distant due to guilt. Alex will get support in this.

* * *

"Eliza? What are you doing here?" Lena asked when her latest PA showed the elder Danvers into her office.

"I was hoping to see Kara." Eliza said. "J'onn said she was here."

"You checking I haven't killed her?" Lena asked defensively.

"No." Eliza said. "Kara trusts you and that's enough for me. I'm just concerned about Kara. She isn't coping well with the Alex situation."

"The Alex situation? That sound like a phrase my mother would use." Lena pointed out. "Does Alex really have no idea about Kara?"

"No. And I don't know what Kara has told you, but in order to erase all the memories of Kara being an alien J'onn got rid of most of Alex's childhood memories of Kara and it has damaged their relationship. Which is why I'm worried about Kara. Unsurprisingly she has always struggled with loneliness. So can I see her?"

"Of course." Lena said digesting everything Eliza had said. "I'll take you down." She added as she stood and walked Eliza out of the office to an elevator.

"How is she?" Eliza asked.

"Withdrawn." Lena said. "She's changed. It's like she lost her spark."

"I should have come down when I heard about the memory wipe. Maybe I could have stopped all this." Eliza said feeling helpless as the elevator doors opened.

"Sweetie." Eliza greeted when she saw Kara.

"Eliza? What are you doing here?" Kara asked as Eliza drew her in for a hug.

"I missed you and I was worried about you." Eliza said squeezing her tightly.

"You saw me three days ago." Kara reminded her.

"So I know I am right to worry."

"I'm fine." Kara said.

"You don't have to pretend in front of me." Eliza said refusing to release her.

"I know." Kara said relaxing into the embrace.

-00-

"Mom? What are you doing here?" Alex asked when she found Eliza waiting outside her apartment.

"I was in the area and thought I'd stop by." Eliza said. When Alex didn't make an effort to open her front door Eliza said. "Are we going in?"

"Um, how about we go out?" Alex countered. "I'll buy you dinner."

"Okay." Eliza said wondering what Alex was hiding.

"So why exactly are you in National City?" Alex asked as they rode down in the elevator.

"My lab is thinking of buying some new equipment. L-Corp is one of the providers so I wanted to talk to Lena."

"How'd that go?" Alex asked.

"Fine. Why do you ask?"

"Lena and Kara had a falling out."

"About what?" Eliza asked, unsure what Kara had told Alex.

"No idea."

"You didn't ask?"

"No. I mean it's not like Kara told me. Brainy did." Alex replied. The statement surprising Eliza.

-00-

"So were the lab supplies the only reason you came to National City?" Alex asked as they sat at a table.

"No. I was worried about you."

"Me? I'm fine." Alex said not looking up from the menu.

"No you're not. What is it?"

"I don't know. I just feel like there is something missing."

"Missing?" Eliza asked.

"I don't know, it's just a feeling. It's like when you go to the shops to buy something but when you get there you don't know what." Alex said as she downed a drink. "I have that feeling the whole time. And no matter what I do I can't shake it. The worst part is, I feel like it is affecting my work. It's like I'm not as efficient and my judgement isn't right."

"Does it have something to do with Supergirl?" Eliza asked carefully.

"No. If I repeated the situation I would do the same. All the intel pointed to Supergirl being a murderer. I thought Supergirl was about to kill me." Alex said. "Colonel Haley, even the President have described it as a good kill. As much as I hate the term, I know logically I did the right thing."

"But?"

"But something feels off." Alex said. "But it's not just Supergirl, it's been going on for weeks."

"Did you talk to Kara about it?"

"Why would I?" Alex asked confused.

"Because she's your sister."

"That doesn't seem to mean much any more." Alex said. The statement once again taking Eliza by surprise. "I mean she isn't even taking my calls right now. Maybe we were never that close. I mean she has never talked about her real family or what happened to them." She added as her phone buzzed.

"Sorry, I have to go." Alex said.

"Look after yourself." Eliza replied wondering if Alex and Kara would ever be able to get back what they had.

-00-

"I think I've found something." Lena said.

"What?" Kara asked.

"I think the other you was created as a result of you using the Harun-El."

"What do you mean?"

"I think it kind of split you."

"Can we use the Harun-El to un-split us?" Kara asked.

"I'm not sure it is that simple. I have been running some simulations and the longer you have been split the less likely it is you can recombine. There are four possible outcomes and based on how long you have been split rejoining is not the most probable result."

"What are the others?"

"One, you over power her and you survive she doesn't like Sam did with Reign. Two the same but opposite. And three, the most likely is the interaction kills both of you."

"How likely is it that she over powers me?"

"About fifteen to twenty percent."

"So there is what an eighty percent chance that if I use the Harun-El we stop her?" Kara asked.

"Yes, but there is still a greater than sixty percent chance you don't make it out alive."

"It's worth the risk." Kara said.

"What happened to Supergirl doesn't kill?" Lena asked.

"You said it yourself, I'm a hypocrite." Kara said. "How long until you have the piece of the Harun-El that is ready to use?"

"I already have it." Lena said.

**-TBC...**

* * *

**A/N:** Thanks for reading and reviewing.


	6. Chapter 6

**A/N:** Thank you for the comments

Kira007Goddess o - Thanks for the ideas. For once I have already finished writing this story so won't be able to incorporate the ideas into the coming chapters. But there will be drama in this chapter.

Guest (1) - Thanks! I'll try to keep posting daily.

Guest (2) - James definitely didn't help the situation.

* * *

"I really didn't expect you to recover so soon." The alternate Supergirl said as she landed in front of Alex and punched her to the ground before she could draw her gun. "I mean throwing yourself into work is very you, but, I have to give you credit for being so heartless. I thought killing Supergirl would have destroyed you, but you took it better than killing Astra." She continued as she walked over to Alex and took her gun. "We don't want any accidents. Especially when I have so many questions for you."

"Leave her alone." Supergirl said landing behind Alex.

"Supergirl? How?" Alex asked looking as confused as the alternate version at Supergirl's presence.

Ignoring the question Supergirl stepped towards the pair and demanded.

"Leave Alex alone."

"How pathetic." The other version said. "She tried to kill you and yet the second she is in trouble you come running back like a faithful dog. You mean nothing to her. So why are you here?"

"I will always protect Alex." Kara said.

"Well you suck at that." The other one laughed pointing at the fallen Agent who lay on the ground watching confused. "I am curious about how you survived, but more curious about what happened to her for her to forget you?" She said pointing at Alex.

"It doesn't matter." Kara said punching the other Supergirl. Turning to Alex she said. "Go. It's not safe. And Alex, none of this was your fault." She added before flying towards the other Supergirl and grabbing hold her, flying them both as far away from Alex as possible.

As the other Supergirl fought back they both crashed into the ground. Seizing her opportunity Kara removed the Harun-El from the pouch Lena had made, and forced the other version to hold the rock. As the two of them simultaneously gripped the rock, the rock started to glow before they both disappeared in a bright flash.

-00-

"Easy." Haley said when Alex tried to sit up.

"Colonel? Where am I? What happened?"

"You are back at the DEO. You were knocked out by the blast."

"The blast?" Alex asked. "Wait Supergirl is alive."

"Was alive." Haley corrected.

"No, she was there. She saved me." Alex said.

"Yes, but in doing so it looks like she killed herself and the other version."

"I don't understand."

"I don't pretend to understand it all myself." Haley said. "All I know is despite being apparently dead, she returned to the living and saved you. Only after she saved you she flew herself and the other Supergirl a short distance away and then apparently blew them both up. No bodies were found, but according to our walking calculator the chance of either Supergirl surviving an explosion of that magnitude is less than zero point one percent." She explained before noticing Alex looking distant. "Director Danvers are you okay?"

"I'm fine." Alex said, sounding confused as she started to get up.

"Where are you going?"

"Home."

"You have a concussion."

"I'm fine."

"You're not leaving unless I know there is someone to take care of you." Haley said when Alex didn't respond she asked. "What about your sister?"

"She's out of town." Alex said.

"The Martian?"

"We aren't exactly speaking after I killed Supergirl." Alex said.

"Looks like you are staying here then." Haley said. "Get some rest." With that she left Alex alone to replay events in her head.

-00-

"Danvers." Maggie said as she sat opposite Alex in the alien dive bar the following evening.

"Sawyer." Alex slurred. "What are you doing here?"

"Word on the street is you've had enough, but Crax is too afraid to tell you so called in a favour and asked me."

"I'm fine." Alex said.

"The drink tells a different story. So what's up?"

"I think I'm missing something." Alex said.

"Something?" Maggie asked.

"Yeah. Something is missing. Something big… but don't know what. I thought it was a kid, now I'm not so sure." She said downing another shot.

"Does it have something to do with what happened yesterday with the two Supergirls?"

"No. Before that. The last few weeks… There's been a hole. I'm missing something. Don't know what though. But maybe it is related...I mean what did she mean, it's not my fault? I don't get it. Why can't I remember things?"

"Things?"

"I don't know, I know there are things I don't know. But I should know. And then that other version talked about me forgetting. It makes no sense. And why would Supergirl say she'd always protect me?" Alex asked before noticing the slight twitching on Maggie's face. "You know something."

"No."

"I know you and I can tell when you are hiding things." Alex said pointing an accusatory finger at Maggie, only she was so drunk she pointed at a spot a foot to the left.

"Not when you are this drunk." Maggie deflected before asking. "Is Supergirl really gone?"

"Yeah, they both are. No way to survive that explosion." Alex slurred.

"Have you spoken to your mom recently?" Maggie asked.

"No. Should I have done? Wait did I miss her birthday?"

"No. I just think you need to talk to her."

"That doesn't normally end well, especially after I've had a drink."

"I didn't mean now. Let's get you home and sobered up. Then call your mom."

-00-

"Maggie?" Eliza asked surprised when she saw the Detective half drag Alex into the apartment.

"Eliza, hey." Maggie said awkwardly before explaining. "I got called to the bar to take Alex home."

"Mom? What's going on?" Alex asked straightening.

"We'll talk in the morning when you are less drunk." Eliza said taking Alex's other arm and helping Maggie get Alex to the bedroom.

"I'm not drunk." Alex protested.

"Of course not." Eliza said as she and Maggie managed to get Alex to sit on the bed. As soon as she was unsupported she fully collapsed and fell to sleep.

Awkwardly moving her into a semi-comfortable position Eliza placed a blanket over her before leaving the bedroom with Maggie.

Without focusing on carrying Alex Maggie could take in the state of Alex's apartment which looked like a tornado had ripped through it. What concerned her more was the number of empty scotch bottles around.

Turning she faced Eliza and took in her pale appearance and bloodshot eyes.

"Is she really gone?" Maggie asked.

"Yes." Eliza said, struggling to keep her voice flat.

"I'm sorry." Maggie said. "Is there anything I can do?"

"Thank you, but no."

"Are you going to tell Alex the truth?"

"That's one of the reasons why I'm here." Eliza said before asking. "Do you know what caused the drinking tonight?"

"She said she feels like there is a hole in her." Maggie said. "I'm sure J'onn had his reasons but this memory thing has really messed her up."

"I know." Eliza said. "I worry that finding out the truth will break her."

"It's going to be better hearing it from you than anyone else." Maggie said.

**-TBC...**

* * *

**A/N:** Thanks for reading and reviewing.


	7. Chapter 7

**A/N:** Thanks for the comments.

Guest (1) - It won't be long before a kind of explanation of what happened to Kara is given.

Guest (2) - Nia is Kara's friend and so believed in her. Now Nia is recognising dreams are symbolic rather than literal I don't think she would necessarily assume Supergirl is bad no matter what she sees. Also they have had the Bizaro plot and the Red-K plot so for no one to believe there wasn't a different explanation would be weak. Lena isn't making a weapon designed to kill Kara, she is trying to help humans. And presumably if James doesn't tell Kara she should be mad with him when she finds out he knows.

Guest (3) - Sleep will not be Alex's friend.

* * *

"Alex? How are you feeling?" Eliza asked as Alex stumbled to the kitchen.

"Mom? What are you doing here?" Alex questioned wondering how much she had had to drink and if she was still drunk. Ignoring her pounding head she looked at her mother and noticed her red eyes. "Have you been crying? What's happened?"

"Come sit down." Eliza said. Confused Alex dropped down next to her before being pulled in for a hug.

"What's wrong?" Alex asked growing increasingly concerned. "Do you want me to try and call Kara?" The question causing Eliza to hold her tighter.

"Has something happened to Kara?" Alex asked pulling away.

"She's gone." Eliza said trying to keep composed.

"Gone?" Alex asked confused.

"She's dead Alex."

"No." Alex said looking at Eliza who was struggling to hold it together. "I don't understand. How?" Alex asked. "This is my fault. I shouldn't have let her go on a long assignment. God I don't even know where she went on assignment."

"Alex, Kara wasn't on assignment."

"Yeah she was. That's why she's not been around." Alex argued.

"No it's not." Eliza said before stating. "Kara was Supergirl."

"I thought I was the one drinking last night. Kara wasn't Supergirl. Supergirl is, was, a fearless alien. Kara was, well, Kara. There is no way I wouldn't know that she was Supergirl."

"To protect Kara you asked J'onn to wipe your memories of Kara being Supergirl." Eliza said as J'onn flew through the window.

"I'm not sure what has happened to you, but you're scaring me." Alex said. "I'd know if my dorky sister was an alien. I mean for starters she can't lie."

"This might make things clearer." J'onn said handing her his phone. "You made this video just before I performed the memory wipe." Confused Alex took the phone and pressed play.

"Colonel Haley is about to use an alien to uncover Supergirl's real identity. When she finds out we already know she will blackmail her into following every order she issues. I and everyone else at the DEO who knows can't allow that to happen. So we have all asked J'onn to erase the memories we have that will reveal her identity. This was my idea and I know how hard it will be for her. But it is the only thing I can do to protect her. I just hope it works. Oh and Kara wanted you to know that I gave her permission to lie to you, well us. She already feels guilty about it."

"Give them back." Alex said looking at J'onn.

"It's not that easy." J'onn said.

"Give them back." Alex growled.

"I erased them." J'onn said.

"From me. But you have them, you have to because how else would you know what to erase. You must have scanned my mind and found the memories to erase, but you wouldn't have just erased them, you would remember what you saw."

"Is that true?" Eliza asked.

"In a way."

"So give them back." Alex said.

"Is it not that simple, your mind may not be able to cope with the transfer."

"Try." Alex growled.

"Alex, it could kill you or destroy your brain."

"I don't care. Give me back my memories." Alex demanded. Glancing at Eliza J'onn saw the fear and pain in her eyes and said.

"What happens if it goes wrong? Who will look after your mom?"

"That's low." Alex said. "I need them back. Please."

"Do it." Eliza said hating to see Alex so distraught.

"Okay, sit down." J'onn instructed before he sat opposite her and placed his hands on her head as Eliza looked on concerned.

As Alex remembered everything she had forgotten she also recalled her actions from the previous few weeks including trying to kill Supergirl and then Supergirl's death. Paling, Alex jumped up and ran to the bathroom where she threw up.

Following her Eliza rubbed her back until Alex had nothing more to throw up. She then pulled Alex into her arms and said. "Alex, it wasn't your fault. You were trying to protect your sister."

"And in doing so I broke her then tried to kill her. She died believing I hated her." Alex said crying.

"Kara knew you loved her." Eliza said holding Alex tighter.

-00-

Opening her eyes she was immediately aware of feeling sick and dizzy. Then as she tried to move she realised she was chained to a slab. Struggling to free herself she pulled at the chains but couldn't break them, her strength depleted.

"They won't break and you are surrounded by Kryptonite." A voice said as it approached.

"Lena?" Kara asked forcing her neck round. "What happened?"

"I'm not entirely sure. You tell me. What do you remember?"

"I was fighting with the other me, she was trying to kill Alex. I forced her to grip the Harun-El like you told me to."

"And then?"

"I woke here."

"You don't remember anything in-between?"

"No. What happened? Where is the other me?"

"No idea. After you both held the rock you disappeared."

"Disappeared?" Kara asked. "What do you mean?"

"You both vanished into thin air accompanied by a huge explosion." Lena said. "The best theory anyone could come up with was a kind of meeting of matter and anti-matter. One that was so powerful it disintegrated both of you. But I didn't believe it so I came back here. It is where you and Reign fought for the last time. The place where you last used the Harun-El" Lena said. "And here you were, unconscious but alive."

"Who chained me up?" Kara asked.

"I did."

"Why?"

"Because I don't know who you are. You could be Supergirl, you could be the evil version, you could be a different version altogether." Lena said.

"It's me." Kara said. "You know me."

"That's kind of debatable." Lena pointed out. "I never knew you. Even if I did, the other version was intelligent and knew enough about you that I have no doubt she could put in a very convincing performance as you."

"Then kill me." Kara said.

"What?" Lena asked surprised.

"You're right there is no way to tell if I am me. We don't know what happened, we may never know. The two of us could have merged together and it could be like Sam and Reign. We can't risk the other version getting out. So kill me. The world already thinks I'm dead. What difference would it make?"

"You want me to kill you?" Lena asked.

"Yes. No. I can't put that on you." Kara said. "Can you give me a pill or something. I'll take it. I'll be the one responsible."

"You're serious?" Lena asked eyes wide.

"Yes."

**-TBC...**

* * *

**A/N:** Thanks for reading and reviewing.


	8. Chapter 8

**A/N:** Thanks for the comments.

Guest (1) - Things will eventually get a little brighter.

Guest (2) - Quite a few people have died by Alex's hand, including Astra to 'save' J'onn, yet Kara forgives. I was assuming seeing herself on the video would have been a give it was from her (or J'onn). Most of the times I have been with people when they have lost a loved one the reaction is shock and silence, not screaming 'no', so rightly or wrongly I went for that. Alex will react more strongly later. There isn't much need in fixing the other agents as their memories of Kara weren't as deep rooted so they probably don't know anything is wrong. The Children of Liberty are still around in this.

Guest (3) - I also hope on the show the memories aren't gone forever. Although options for getting them back seem limited.

* * *

"I had one job, to protect her. I failed." Alex said bitterly as she sat on the couch hugging her knees.

"Erasing your memories was to protect her." Eliza reminded her.

"Well that didn't work did it. All it did was make her miserable and then kill her." Alex said going to the kitchen and opening her cupboards.

"I threw it out." Eliza said guessing what she was looking for.

"All of it?"

"There wasn't much left." Eliza pointed out. "Getting drunk isn't going to bring her back."

"You think I don't know that?" Alex asked angrily before immediately apologising. "I'm sorry. This is my fault not yours."

"It's not your fault." Eliza said moving over to Alex and hugging her.

"Yes it is. I killed her, then I justified it to everyone, including you." Alex then paused before looking up and asking. "You knew I hadn't killed her?"

"Yes. After you shot her J'onn brought me to the Fortress of Solitude where she was recovering."

"I can't imagine how hurt she was." Alex said pulling out of her mother's embrace and going to the couch again. "Why did she come back? She could have gone to Argo City and been safe."

"J'onn suggested it. But she refused to leave while you were in danger." Eliza explained. "I know you are hurting right now, but Kara did what she did so you could live and be happy. And I know that seems impossible right now, but if you give into the darkness inside you she will have died for nothing." She then watched as Alex sat lost in thought. Finally Alex looked at her and said.

"I blamed her so many times for what happened to dad. But I'm the one who has ruined our family."

"No you're not." Eliza said once again pulling Alex into her arms. "Any one of us could have told you the truth at anytime. But we didn't."

"Why didn't you?" Alex asked.

"It was Kara's choice." Eliza said. "At first to ensure Haley didn't find out. Then she thought you would be happier not knowing. She thought that when you found out you would go back to trying to protect Supergirl and she wanted you to be free from that." Eliza explained once again causing Alex to silent sit and think. Finally Alex pulled out of the embrace and asked.

"Can we go back to Midvale?"

"Of course." Eliza said, surprised by the request.

-00-

As Kara lay, chained to the ground, she heard a noise coming from the side.

"Lena?" She called, feeling scared and vulnerable.

"I'm here." Lena confirmed as she approached the Kryptonian.

"I thought you had gone for good." Kara said.

"I needed time to think." Lena said. "Even if I don't make you take the pill I would still be responsible for your death."

"No you wouldn't. This is on me, not you." Kara argued.

"Life is not as black and white as you'd like to think." Lena countered. "And I am not as heartless as you think."

"I've never thought you were heartless." Kara said. "And I hate asking you to do this. But you said yourself there is no other way."

"That's not what I said." Lena pointed out.

"Maybe not word for word, but we both know that's what you meant." Kara argued.

"Okay." Lena said handing Kara a bottle of water and a pill.

"Will it hurt?" Kara asked looking at the green pill.

"No." Lena said. "You might start feeling drowsy, but there won't be pain. Eventually you'll fall to sleep and just not wake up."

"I know I have no right to ask this. But will you stay with me?" Kara asked. "I don't want to be alone."

"I'm not going anywhere." Lena said as Kara swallowed the pill.

"Lena, I am sorry for everything I did to hurt you."

"I know."

"Will you keep an eye on Alex?"

"Of course." Lena replied before Kara finally shut her eyes and drifted to sleep.

-00-

"She's really gone this time?" Nia asked as she hugged her knees.

"It appears so." Brainy said.

"I keep hoping I'll have a dream that proves you wrong." Nia said.

"So do I." Brainy confessed.

"I miss her."

"I know."

"How's Alex?" Nia asked looking up.

"Last I heard intoxicated at the alien dive bar. Eliza was coming to look after her and tell her the truth."

"Sometimes I really hate this world." Nia said.

"Me too."

-00-

"Lena?" Kara asked confused when she woke up.

"Kara."

"Did it fail?" Kara asked.

"No."

"Then why aren't I dead?"

"Because that wasn't the plan."

"I don't understand."

"I wasn't sure that it wasn't the other you. I assumed she wouldn't actually want to die so wouldn't take the pill, whereas you would."

"So it was a fake?"

"It was." Lena confirmed. "You are fine and free." She said causing Kara to realise she was no longer chained and the Kryptonite had gone. Lena let Kara process everything for a few minutes before asking. "What are you going to do now?"

"Disappear." Kara said. "Everyone thinks I'm dead anyway."

"What about Eliza and Alex?" Lena asked.

"They can move on. Without me they will be safe. If I go back Alex might figure out who I am and if she works that out I don't know how she'll react to nearly killing me."

"Supergirl being dead is one thing. But you were Kara a long time before you were Supergirl." Lena argued. "Not telling Eliza you are okay, don't you think that is selfish?"

"Yes, but if it means she and Alex will be safe that's okay."

"No it's not." Lena argued. "At least tell Eliza."

**-TBC...**

* * *

**A/N:** Thanks for reading and reviewing.


	9. Chapter 9

**A/N:** Thanks for the comments.

* * *

"Still not sleeping?" Eliza asked when she came and sat on the porch with Alex in the early hours of the morning.

"I just can't get over the fact I shot her. If Nia hadn't warned Brainy I would have killed her and I didn't care."

"It wasn't your fault." Eliza said.

"It was, and the worse part is when I replay it, all I can see is the look in Kara's eyes. She looked so defeated so betrayed. I did that."

"Alex, you chose to lose part of yourself in order to protect Kara. That decision can't have been easy and none of you could have foreseen what would happen. I can't imagine how hard it was living when you know something is missing, but you don't know what. You had the same, almost lost, look that your grandmother had towards the end." Eliza said.

"I made so many bad decisions. I betrayed the people I loved. I didn't even follow my own values." Alex said.

"Everyone gets lost." Eliza said. "Normally not because you have had your memory wiped, but you always outperform everyone so why would this be different?"

"Kara died thinking I hated her. She must have been so alone. It's not fair. She didn't deserve that." Alex cried.

"I know." Eliza said hugging her.

"I'm going to go for a run." Alex said feeling undeserving of her mother's love.

"It's five in the morning." Eliza pointed out.

"Perfect time for a run." Alex said. "I'll be back later."

-00-

"Alex? Is that you?" Eliza called when she heard the front door open. Not getting an answer she turned round and saw Kara and Lena.

"Kara? How?" Eliza asked before rushing over and hugging her.

"I don't know exactly, only that Lena saved me. But I'm okay." Kara said pulling away.

"Alex will be so happy." Eliza said hugging Kara again. "When she remembered everything it near broke her."

"Alex remembered?" Kara asked frowning.

"Yes." Eliza said as the backdoor opened and Alex walked in.

"Kara?" She asked paling like she had seen a ghost.

"Alex." Kara replied, uncertainty in her voice.

"Kara. I'm so sorry." Alex said as tears flowed. Not saying anything Kara ran up to her and hugged her.

Noticing Lena slip away Eliza hurried after her.

"Lena wait. How can I ever thank you?"

"I didn't really do anything." Lena shrugged.

"You gave me back my family. That's not nothing." Eliza said before asking. "Where are you going?"

"Back to National City."

"Why don't you stay?" Eliza offered.

"You three have a lot to work through, especially Alex and Kara." Lena said.

-00-

"I'm so sorry." Alex said.

"What happened wasn't your fault." Kara said. "Not even J'onn knew what the mind wipe would do."

"But I still chose to do it." Alex said. "And then I was so mean to you."

"To Supergirl." Kara corrected.

"Who is you." Alex argued. "I am so sorry I hurt you."

"I don't blame you. I'm just so happy you are back." Kara said as Eliza re-entered the room and hugged both of them.

-00-

"I missed this so much." Kara said as she sat on the couch being hugged by Alex that evening.

Not sure what to say Alex just held her tightly.

"There is something good that came from it." Kara said.

"What?"

"Seeing we haven't had a sisters' night in like forever we have weeks worth of TV to binge on and when there is a cliff hanger we don't have to wait for the next episode."

"There is that." Alex conceded as she saw Eliza walk past the room.

"Do you want to join us?" Alex called.

"No. Tonight for the first time in a long time I think I will be able to sleep. I don't want to waste the opportunity." Eliza said entering the room. "Don't stay up too late. You both need sleep too." She added before kissing them both goodnight.

"I know I've not shown it recently but I love you and Supergirl you." Alex said.

"I love you too." Kara said. "I've missed you so much."

"I'm sorry." Alex repeated.

"It's not your fault." Kara said. "You lost your memory protecting me."

"And in doing so I hurt you."

"What matters is you are back to being you." Kara said.

-00-

When Eliza came down early the next morning she was surprised to hear voices from the kitchen. What surprised her most was the carnage that greeted her as she entered the kitchen which was covered in flour. A sight that was mirrored on Alex and Kara.

"What's going on?" Eliza asked.

"Mom? You're up?" Alex said surprised.

"Well it's after six."

"Already?" Alex asked looking at her watch.

"What happened in here?" Eliza asked.

"Um, we wanted to make you breakfast so we tried to cook pancakes, only didn't have the pre-made ones so we tried from scratch." Kara explained.

"Thank you?" Eliza asked unsure what she was meant to say.

"Turns out we still can't cook." Alex offered.

"But we didn't actually set fire to anything." Kara said proudly.

"Uh huh." Eliza said before noticing how tired Alex was looking and asking. "Did you two actually go to bed last night?"

"No." Alex confessed.

"Why don't you two go get cleaned up and I will make some edible breakfast? Then you can both get some rest." Eliza suggested.

-00-

"Where's Alex?" Kara asked when she came down after her shower.

"She went for a run."

"Before breakfast?" Kara asked.

"She said she needed to think."

"Which means she's blaming herself or me." Kara said sadly. "I'm going to find her."

"You don't know where she went." Eliza pointed out.

"Yes I do." Kara replied before leaving.

-00-

"Kara? What are you doing here? How did you even know I was here?" Alex asked when she saw her sister approach her as she sat in the woods.

"It's your go to place for when you want to be alone." Kara said coming to sit next to her.

"How do you know about it?"

"When you started disappearing after Jeremiah's funeral I was worried about you so I followed you."

"You never said."

"Well when I got here you were pacing and talking to yourself complaining about me so I didn't think you'd want me around."

"I didn't mean what I said back then." Alex said. "I was angry."

"I know. But you also needed space so I stayed away. But I can't do that any more. I get that you are angry at me b-"

"I'm not angry at you." Alex said. "Why would I be angry with you?"

"Because I lied to you."

"About what?" Alex asked confused.

"Being an alien, being Supergirl."

"I gave you permission."

"I hurt you." Kara said taking hold of Alex's hand that still had a faint scar from Kara's heat vision.

"Well I did deserve it." Alex shrugged. "I am the one who needs to apologise. I tried to kill you."

"You thought I was trying to kill you." Kara argued.

"Only because I couldn't remember who you were which was my fault as the mind wipe was my stupid idea."

"Which you did to protect me, like you always do."

"It was a mistake. One that I can never take back. I don't know how to make it right."

"I just want my sister." Kara said hugging Alex.

**-TBC...**

* * *

**A/N:** Thanks for reading and reviewing.


	10. Chapter 10

**A/N:** Thanks for the comments.

Guest - yeah the mind wipe was flawed. In this there is still angst to come for Alex.

* * *

Having finally got her kitchen not looking like a war zone Eliza was just about to make some coffee when the doorbell rang. Drying her hands she went to the door and found an unexpected trio waiting.

"J'onn, Clark," she started before recalling the photo Kara had shown her and asking. "Alura?"

"Eliza." Clark said before hugging her. "We came as soon as J'onn told us. How are you holding up?"

"She's not dead." Eliza said bluntly, wanting to put Alura out of her misery as fast as possible.

"She's not?" Clark asked confused.

"No. Lena found her." Eliza said. "I don't know all the details, but I do know she is alive."

"Where is she?" Alura asked, finding her voice.

"She's out with Alex, but they'll be back soon." Eliza explained. "Why don't you come and wait inside?"

"She's really alive?" J'onn asked as shocked as everyone else as they walked to the lounge.

"Yes." Eliza confirmed.

"Is she okay?" Clark asked as they sat down.

"She's pretending to be. But it's going to take time." Eliza said as the back door opened and they heard Alex say.

"You are such a dork."

"Me? How many science fairs did you drag me to?" Kara asked.

"Clearly not enough." Alex pointed out before calling. "Mom?"

"We're in here." Eliza called back.

"We?" Alex asked tensing. Putting an arm out she stepped in front of Kara and entered the lounge first ready to fight any threat she might face.

"Mom? Kal? What are you doing here?" Kara asked as she followed Alex in and saw her Kryptonian relatives. Instead of answering Alura just engulfed her in a hug.

-00-

"How are they doing?" J'onn asked as he came and stood next to Eliza who was watching her daughters from a distance.

"I don't know. They are both pretending to be strong, but they are both carrying so much pain."

"I'm sorry for the part I played in that." J'onn said sadly.

"You and Alex both thought you were doing the right thing." Eliza said, trying to keep her anger buried and sound more charitable than she felt.

"How bad is the situation on Earth?" Clark asked as he joined them.

"Bad. The hatred keeps growing and there doesn't seem to be an end to it." J'onn said.

"Is Kara in danger?"

"No more than any other alien."

"Would it help if I came back?"

"I doubt it. Plus it would add to Kara's guilt complex if she thought she was responsible for you leaving Lois." J'onn replied.

"Is there anything we can do?" Alura asked walking towards them having listened to the entired conversation.

"Right now the word needs Supergirl to be the beacon of hope that she was when she first came out. For that to happen Kara needs to find her hope and optimism again. For that she needs Alex." J'onn listed.

"What's going on?" Kara asked as she and Alex walked in and saw everyone assembled.

"I was just thinking about making lunch. Are you hungry?" Eliza lied.

"Always." Kara replied although she looked at the group like she didn't believe the story.

"Why don't you show Alura some of the photos while I put the food on?" Eliza suggested.

-00-

"This one is from my third summer here." Kara said holding a photograph as she took Alura through her history on Earth. "Alex had dragged me to loads of science fairs, but eventually she agreed to take me to the art fair. It reminded me of the fair we used to go to in Morton." Kara recalled happily. "There was a sculptor there who made these carvings of mythical animals, only one was just like the ragloons back home."

Realising she couldn't remember the event that Kara was talking about Alex slipped out of the lounge and ran outside the house.

"I've got it." J'onn said to Eliza as he followed Alex out.

-00-

As Alex came to a stop she saw a tree and started unleashing punches on it.

"The tree isn't to blame. I am." J'onn said walking up to Alex.

"It was my idea." Alex said turning.

"And I agreed to it. I could have, should have, said no." J'onn said. "I'm sorry."

"I'm responsible, not you." Alex said punching the tree again.

"Punching trees won't change what happened." J'onn tried.

"I know, but it makes me feel better." Alex said ignoring the throbbing pain in her hand.

"What's wrong?" J'onn asked.

"There are still holes." Alex confessed. "I'm still missing pieces of my life and I don't know if they are important. What if Kara gets hurt as a result of the holes?"

Not knowing what to say J'onn pulled Alex in for a hug.

-00-

"What happened to your hand?" Eliza asked when she saw Alex open the freezer and put an ice pack on it.

"I fell." She lied.

"You have to go to hospital." Kara exclaimed.

"I'm fine." Alex replied.

"You have three breaks in you fingers and a crack in your hand." Kara pointed out having assessed the damage using her x-ray vision.

"Come on, I'll take you." Eliza said.

"I'm fine." Alex protested.

"Alexandra, get in the car." Eliza instructed.

"Fine." Alex said giving up.

**-TBC...**

* * *

**A/N:** Thanks for reading and reviewing.


	11. Chapter 11

**A/N:** Thanks for the comments.

Chloe - There is no easy fix for Alex in this, but Kara and Eliza will rally round her.

* * *

"Where are we going?" Alex asked when she noticed Eliza turn the wrong way out of the hospital car park.

"I thought we'd go for a walk."

"A walk?" Alex asked.

"Well you are not meant to drink with the painkillers." Eliza reminded her. "And if we went for ice cream without Kara we would never hear the end of it. And seeing you are not sleeping coffee is a bad idea, so a walk seemed like a good idea."

"Why aren't we going back to the house?" Alex asked.

"Because you need to talk to someone without Kara listening in."

"I'm fine."

"You punched a tree." Eliza pointed out. "Probably more than once."

"How did you know?" Alex asked, not bothering to deny the claim.

"You had splinters in your hand." Eliza pointed out.

"Well I was angry and frustrated." Alex said looking down at the cast on her hand.

"About?"

"My ability to screw up life."

"You don't screw up life." Eliza said.

"The first time I met J'onn I was in a jail cell." Alex confessed almost causing Eliza to swerve off the road.

"Why?"

"Attempting to drive while intoxicated."

"Does Kara know?"

"No. Well I don't think so. I haven't told her. Or at least I don't remember telling her, but I guess that doesn't mean much." Alex said. "But if she knew she would have ended up telling you, so I doubt I told her."

Not knowing how to respond Eliza silently waited for Alex to continue.

"My life was spiralling out of control because of my own inability to control it and J'onn saved me. J'onn has always been there for me, looking out for me. And then I made him wipe my memory and now he is feeling guilty." Alex said as Eliza pulled off the road. "I remember this place. I haven't been here for years."

"Do you remember the last time?" Eliza asked.

"The weekend before Kara came." Alex said after a moment before paling and asking. "Or have I forgotten coming here with Kara?"

"No. You never came here with Kara. But it used to be your favourite place."

"Yeah, we'd all come here and have a picnic. Then we'd kick a ball around. And you and dad would teach me about the different birds." She listed before adding guiltily. "Kara would have loved it. But I refused to come back."

"You said you were too old for it." Eliza said.

"I lied. I just didn't want to share it with Kara." Alex confessed.

"I know."

"You knew? Why didn't you force me to come?"

"You had just had your life turned upside down, we didn't want to force you." Eliza said. "Plus you had just lost your bedroom, you needed somewhere that was yours. And we hoped that you and Kara would find somewhere that could be special for both of you. Which you did."

"So why are we here today?"

"It holds good memories for me too. I wanted to reminisce." Eliza said getting out of the car. "And it is free from trees so hopefully you will just talk through your problems rather than punch through them." She added as she waited for Alex to join her before they started to walk silently through the park.

"What if I don't get them all back? What if a gap causes me to hurt Kara?" Alex eventually asked.

"You would never hurt Kara."

"I tried to kill her." Alex reminded her mother.

"You never hurt Kara, you tried to hurt Supergirl."

"Who is Kara."

"But you didn't know that." Eliza said. "You thought Supergirl was a threat."

"J'onn told me she wasn't and so did Kara, but I ignored both of them and went with my instincts which were completely wrong. How can I trust anything I do? How can Kara trust me? What if how I was when I had the mind wipe was who I really am?"

"Alex you were acting on incomplete information."

"Precisely. And I still don't know if I have the complete information. If I make a decision based on what I think I know, but is actually not correct I could hurt Kara."

"Alex, there is no way of knowing if all your memories are there."

"They're not." Alex said sadly. "I can still feel the holes. They're not as big as before, but I know something is missing. Like earlier when Kara was talking to her mom about that art fair, I couldn't remember it."

"They may come back. But even if they don't you are going to make new memories and until you trust yourself trust those around you."

-00-

"I don't know how you do it?" Kara said to Kal as they sat on the bench in the garden.

"Do what?" He asked.

"Take on the world alone."

"I'm not alone. I have Lois." Clark said confused.

"Yeah, but she doesn't stand by your side when you go and fight someone." Kara said.

"Something I am thankful for every day." He said. "But in answer to your question, fighting alone was something I have always had to do. I got used to it." When Kara didn't say anything he asked. "Why didn't you come to me for help?"

"Lois needed you. And I guess maybe pride. I mean you left me for a few months and I broke the world."

"You didn't break the world." Kal said wrapping an arm round her as Alura came to join them.

"Are you two okay?" She asked.

"Yes." Kara said pulling away from her cousin and looking at her mother.

"I am happy that you never lost your inability to lie." Alura said sitting next to Kara. "But you do not need to lie to me."

"I'm okay. I have to be." Kara said.

"What does that mean?" Alura asked confused staring at Kara until she started talking.

"Alex feels so guilty for what happened. But everything that happened was a result of her making another sacrifice to protect me." Kara explained. "You've both seen how guilty she looks even though none of it is her fault. If I tell her I'm not okay she will blame herself even more. She doesn't deserve that. She has always been so strong and looked after me. Now I need to be strong for her."

"And for that I am so proud of you." Alura said pulling Kara in for a hug. "But right now Alex is not here. You don't need to be strong in front of us."

-00-

As Eliza and Alex walked into the house they were met with a smell of fresh cooking. Confused they went to the kitchen where J'onn was standing in front of a saucepan stirring something.

"J'onn?" Eliza asked.

"Hi. How's the hand?" J'onn asked looking at Alex.

"It'll be fine." Alex said before asking. "Why are you cooking?"

"It was getting late and there are three Kryptonians here. I also thought Eliza might not want to cook so I prepared dinner." He then looked at Eliza and said. "I hope you don't mind."

"Of course not. Thank you." Eliza replied as Kara rushed into the kitchen.

"Alex, are you okay?" She asked as she hugged her.

"I'm fine. You saw yourself it is just a break." Alex assured her.

"Four breaks." Kara corrected.

"Kara, I'm fine." Alex repeated.

-00-

"You stay up all night watching these movies?" Alura asked as she sat next to Kara on the couch.

"Yes." Kara said. "Normally with popcorn, ice cream and chocolate." She added pointing to the coffee table that had all the food on it.

"You mentioned those last time I was on Earth. They are full of sugars aren't they?" Alura asked.

"That's why they taste so good." Kara pointed out.

"Should you eat them at night? Do they not disrupt your sleep?"

"The point of movie night is to watch movies, not sleep." Kara explained.

"Shouldn't you two get some sleep tonight?" Eliza asked.

"We're fine." Alex said.

"So what are we watching?" Eliza asked knowing she wouldn't win the argument.

"Kara's favourite." Alex said causing Kara and J'onn to tense slightly. Oblivious to the looks Kara and J'onn were exchanging Alex dug one handed through the DVDs before pulling out the Wizard of Oz box.

**-TBC...**

* * *

**A/N:** Thanks for reading and reviewing.


	12. Chapter 12

**A/N:** Thanks for the comments.

Grace - Hey, I like that idea, but the timing is not great I'm going to be disappearing for awhile and won't be able to write. So if I did write it, it probably wouldn't be done for about 6 weeks.

* * *

"What are you doing up?" Alex asked when Kara came and sat next to her on the beach early the next morning.

"I could ask you the same thing." Kara said leaning against Alex.

"I couldn't sleep." Alex shrugged as she watched the waves crash into the beach.

"Me too." Kara said. "How's your hand?"

"It's fine. I've had worse. Although don't tell mom that." Alex replied.

"I'm pretty sure she knows." Kara pointed out.

"She merely suspects." Alex said resting her head on Kara's.

"I'm sorry." Kara said after a few moments.

"For what?" Alex asked raising her head and looking at Kara who kept her head on Alex's shoulder.

"Never thanking you."

"For what?" Alex asked growing more confused.

"Everything you have done for me." Kara replied. "When you didn't have your memories and things changed between us it made me realise just how much you do for me and how much I depend on you and I realised I never thanked you for it."

"You don't have to thank me." Alex said as her own guilt rose. "It's what sisters do. What they are meant to do and I didn't do any of that. I was so mean to you. It must have been so hard hearing me talk about Supergirl like the enemy."

"It was fine." Kara lied.

"No it wasn't. It's why you started avoiding me wasn't it?"

"No. Maybe. It was only a small part. I had to keep my distance so you didn't recognise me. I mean you kept walking into my apartment when I wasn't wearing my glasses. But it wasn't just that. I saw it as a way for you to be happy."

"How would you not being there make me happy?"

"I thought if you weren't wasting time with me you could be out there finding the happiness you deserve."

"Kara, being with you is never a waste of time. And all the time you were avoiding me I wasn't happy. I missed you."

"I missed you too. So much." Kara said as she hugged Alex.

"Why didn't you tell me?" Alex asked.

"Tell you what?"

"That you were Supergirl. I mean after Haley stopped believing someone at the DEO knew, why didn't you tell me?"

"I thought it would make your life easier. You've always had to hide part of your life to protect me. If you didn't know about me you wouldn't have to hide it."

"I don't know who is more stupid, you or me." Alex said.

"I've wondered that myself a few times." Kara agreed.

-00-

"Morning." Eliza greeted as Alura entered the kitchen before saying. "She's on the beach with Alex."

"Is she okay?" Alura asked.

"I don't know. When Kara gets hurt she tends to shut herself off as a way to protect herself."

"And this time she doesn't want to upset Alex." Alura said. "She told me she wanted to be strong for her."

"Well she and Alex are talking which is good sign." Eliza commented.

"With everything that happened I never said thank you for everything you did for Kara, I'm sorry. I really am grateful she found such a loving family. I had a somewhat fractious relationship with my sister. For Kara to gain a sister and then become so close to her, I never dreamed that could happen."

"Kara has given more to this family than we've been able to give to her." Eliza said before she walked over to a cupboard and pulled out a box. "I don't know if you want any of this, but if you do you are welcome to it." She said handing the box to Alura.

As Alura opened it she found photos and drawings.

"It can't give you back the time you lost with Kara, but maybe it can fill in some of the gaps." Eliza said.

-00-

"Do you want me to stay?" Clark asked.

"No, Lois needs you." Kara said.

"So do you."

"I'm fine, especially now Alex is back to being Alex." Kara said.

"Are you sure?" He asked frowning.

"I'm sure." She said hugging him.

"You will always have a home on Argo." Alura reminded her.

"I know. But Earth is my home now." Kara said.

"I love you." Alura said hugging her goodbye. "And remember I am so proud of you."

"I love you too." Kara said clinging tightly to Alura who started to reconsider leaving. Sensing her mother's thoughts Kara pulled back and said. "I'm okay. I'm just going to miss you."

"There is not a day that goes by where I don't miss you." Alura said kissing Kara's head before turning and getting into J'onn's car.

As the car started to reverse Eliza and Alex came out and stood on either side of Kara as she waved them off. Once the car was no longer in sight Eliza wrapped and arm round Kara's shoulders and asked.

"Are you okay?"

"I hate goodbyes." Kara said sadly.

"I know." Eliza said hugging her. When she finally pulled back she asked. "What are you two going to do now?"

"I don't know. Can we stay here a while?"

"You can stay as long as you want." Eliza said pulling both daughters in for a hug.

**-TBC...**

* * *

**A/N:** Thanks for reading and reviewing.


	13. Chapter 13

**A/N:** Thanks for the comments.

Guest - to be honest if they don't fix Alex and kara's relationship soon I probably won't continue watching and writing.

* * *

"Alex? What are you doing here?" Lena asked when Alex walked into her office a week later. "What happened to your hand?" She asked noticing the cast.

"I punched a tree." Alex explained.

"How's the tree?"

"Better than my hand."

"I'm assuming you didn't come here to talk about gardening. So why are you here?"

"Kara is going to see you later and I wanted to make sure it would go well. But then as I was riding the elevator up here I realised how hypocritical it was of me to ask if you were going to hurt her. So instead I just want to thank you for saving her life and being there for her when I wasn't."

"How is Kara?" Lena asked.

"She says she's fine, but she's lying." Alex said.

"Did Kara tell you what happened in the cave?" Lena asked.

"She just said you found her there but she doesn't know how she got there." Alex said.

"Did she tell you what happened after I found her?"

"You brought her to Midvale?"

"Between that. When I found her I wasn't sure if she was Kara or the other version so I chained up and kept her close to Kryptonite. When I explained that to her she said it would be safer for everyone if she died. But she didn't want me to kill her as she didn't want me to have that on my conscience. So I gave her a pill that I told her if she took it it would kill her. She took it."

"I'm meant to protect her and I broke her." Alex said dropping down onto Lena's couch.

"Well, I didn't exactly help her either." Lena replied.

"You saved her. You were the only one who didn't give up on her, whereas I killed her."

"Technically you didn't." Lena pointed out.

"I had no idea Brainy had modified the weapon." Alex said. "When I fired, I fired to kill. Kara knows that."

"You fired in self defence." Lena countered.

"Well if I hadn't had my memories wiped I would have known I wasn't in danger." Alex pointed out.

"I thought you had them wiped to protect Kara?" Lena said

"That didn't work did it." Alex replied angrily.

"While I can't start to imagine what you are going through I do know all about doing something for the right reasons, which turns out badly." Lena said. "You can beat yourself up and withdraw from everyone as you live with self-hate. But in my experience it doesn't help. And I am pretty sure Kara wouldn't want that."

-00-

"Kara?" Nia asked dropping her coffee as she saw her friend walk towards her.

"Nia." Kara smiled.

"How? Is that you?"

"Yes it's me and it's a long story. But I'm back."

"And the other you?" Nia whispered.

"Gone. We think. Unless you've had a dream suggesting she isn't."

"No. No dream." Nia said still confused. "Where have you been?"

"Midvale, with Eliza and Alex."

"How'd that go?" Nia asked.

"Alex has her memories back."

"That's great." Nia said genuinely happy before sobering and asking. "Wait, how is dealing with everything?"

"Badly." Kara said. "But she'll be okay. I'm going to make sure of it."

"And you?" Nia asked.

"I'll be fine." Kara said trying to dismiss her friend's concern. "Anyway I better go see James. I'll see you later."

"Let me know if you need anything." Nia said frowning.

-00-

"Lena? Can I come in?" Kara asked as she opened Lena's office door.

"You've not asked permission before." Lena pointed out.

"I was pretty sure you wouldn't say no before." Kara replied.

"Come in." Lena said watching as Kara nervously played with her sleeves as she approached the desk.

"I just wanted to say thank you for helping us defeat the other me and then for saving me."

"All I did was find you." Lena shrugged. "But I should thank you too."

"For what?" Kara asked.

"Believing in me. I'm not sure anyone has ever believed in me as much as you do."

"You're a good person Lena. I will always believe that."

"Speaking of good people, are you coming back as Supergirl?"

"Eventually. First I need to fix things with Alex." Kara explained. "Anyway, I should go. Thank you for everything." With that she walked to the door, only for Lena to start speaking.

"When I saw the news report of you being dead, it made me realise how much I missed you. I know we have both done things we regret but when you and Alex are you okay perhaps we can get lunch."

"I'd like that." Kara said smiling at Lena before leaving.

-00-

"What's wrong?" Kara asked, noticing how quiet Alex was being that evening.

"I saw Lena today." Alex said.

"You did? She didn't tell me that." Kara said frowning.

"She told me what happened in the cave. How you gave up." Alex said.

"That wasn't it." Kara said.

"Yes it was." Alex countered.

"All I want is for you to be happy. I thought if I wasn't in your life I couldn't ruin it." Kara confessed.

"Kara, you being in my life, you being my awesome little sister makes me happy. When I didn't have my memories I knew that something was missing but I couldn't place it. I thought it was because I had put my personal life on hold again, and I guess it was partly that. But now I have my memories back I know there was more to it than that. It was because I didn't have you." She said as she hugged Kara.

"I will always be there for you." Kara said.

"I know and that gets you into trouble." Alex said.

"Me? You are the one with the broken hand." Kara said looking down at the cast as the two fell into a comfortable silence. A silence that was finally broken by Alex whose voice cracked as she said.

"I don't know how you can forgive me. I shot you."

"You thought I was a killer and that I was going to kill you." Kara said, trying to hide her own hurt. "And if it had been the other me she probably would have killed you. It hurt that you lost all faith in me, but you made the right decision." Kara said.

"No I didn't." Alex said. "It wasn't just that I lost faith in Supergirl. I lost faith. Just like I did with Julia and Purity. When I got my memories back I realised that I have this inner darkness but because of you I've been able to control it. You always see the best in people, I've never been able to do that. But I'm going to try because I really didn't like who I became."

"You're wrong." Kara said. "After the mind wipe you were a little darker and less willing to see the good. But the real you was still in there. And this is the real you." She finished with no trace of doubt in her voice. The comment causing Alex to hug her tighter. "And out there somewhere is someone who is going to see just how special you are and make you happy. But you aren't going to find them if you spend all your time at work or looking after me."

"I spend time with you because I want to, not because I am your babysitter." Alex reminded her. "But Kara, right now I just want things to be right between us. Everything else can wait."

"But after that, I can be your wing woman?" Kara asked hopefully.

"No. No chance." Alex said.

"Why?"

"After the last fiasco? I'd be better taking Brainy."

"That's just mean." Kara pouted. "But fine I won't offer any dating tips."

"Safer for everyone." Alex smiled as the two went back to watching the TV. After a few minutes Alex said.

"Kara?"

"Yeah?" She answered looking round.

"You know I love you?"

"Of course I do." Kara said wrapping her arms round her. "I love you too."

**-The End**

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**A/N:** Thanks for reading and reviewing.


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